My files of bacterial genomes are gff type, whose names all end with .gff. But I can’t run Panaroo with them. How can I run Panaroo with them? Thank you so much.
Welcome @Ph_c_Mai
Hopefully we can help!
I’m guessing that your files are in a collection, correct? If so, then the collection identifiers need to have the .gff extension added on.
Panaroo is a bit special in that it is using the file name for the sample labels, and it is hard coded inside of the original tool to expect the extension! There is a request in to make this work differently but that is still pending implementation.
We have an example in this topic showing how to manipulate your collection identifiers. → Panaroo & PanTA: sample recognition troubleshooting - #3 by jennaj
This can be a bit complicated the first time! Please give this a try, and if you get stuck you are welcome to share your history. We can help you to make the adjustment, then share it back, and then you’ll have a template manipulation to guide you.
Or, if I guessed wrong, you are still welcome to share your history or possibly screenshots would be enough. Capture the full page of the job details page for the error (expand the logs too!) and then a few of the input datasets expanded, plus the output for the Extract element identifiers tool if the data is in a collection.
So, you have some choices! Let us know! 
Hi @Ph_c_Mai,
It seems you have gff files in history, but Panaroo takes a collection of gff files. It does not “see” files, only collection, at least, the current version.
Maybe check this FAQ: Creating a dataset collection
Create a collection (Flat list) via Advanced settings and do not remove file extensions.
Hope that helps.
Kind regards,
Igor